Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS03225 BPHYT_RS03225 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q0KEG0 (807 letters) >FitnessBrowser__BFirm:BPHYT_RS03225 Length = 811 Score = 1266 bits (3275), Expect = 0.0 Identities = 640/811 (78%), Positives = 709/811 (87%), Gaps = 4/811 (0%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 MSN I++KVAVLGAGVMGAQIAAHLINA+VPV+LFDLPAKEGPKN IAL+AIENLKKLSP Sbjct: 1 MSNLIIRKVAVLGAGVMGAQIAAHLINAKVPVLLFDLPAKEGPKNAIALKAIENLKKLSP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 AP G+K++A IQ ANY+DDI L ECDLVIEAIAERMDWKHDLYKKVAPHLA +AIFAT Sbjct: 61 APFGVKDDAQYIQPANYDDDIEKLAECDLVIEAIAERMDWKHDLYKKVAPHLAPNAIFAT 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSITALS+GF +LK+RFCGVHFFNPPRYMHLVELIPTATT+P+ILDQLE+FLT+ Sbjct: 121 NTSGLSITALSEGFSDELKARFCGVHFFNPPRYMHLVELIPTATTRPEILDQLESFLTSV 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 +GKGVVRAKDTPNFIANRVGIFSILAV EA KFG+ FD VDDLTG++LGRAKSATFRTA Sbjct: 181 VGKGVVRAKDTPNFIANRVGIFSILAVVTEAAKFGLRFDEVDDLTGARLGRAKSATFRTA 240 Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300 DVVGLDTMAHVIKTMQDTL DDPF PVY+TPAVL LV GALGQKTG GFYKKEGKAIK Sbjct: 241 DVVGLDTMAHVIKTMQDTLKDDPFFPVYETPAVLAELVKKGALGQKTGGGFYKKEGKAIK 300 Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360 VLD KTG+YVD G ADE+V R+LK+ AER+KLLRES +PQAQFLWA+FRDV+HYI V+ Sbjct: 301 VLDPKTGEYVDGGANADELVGRILKRPPAERLKLLRESEHPQAQFLWAIFRDVYHYIGVH 360 Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420 LE IA +A D+DLAIRWGFGWN GPFE WQ+AGWKQVAEWV+ED+ AGKALS PLP+WV Sbjct: 361 LESIADNARDVDLAIRWGFGWNEGPFEGWQTAGWKQVAEWVQEDIAAGKALSNVPLPSWV 420 Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480 EGPVAE GVH GSWSPA+++FV RS L VY +Q FRA + G ADP+ G+T+ E Sbjct: 421 LEGPVAEQGGVHTNEGSWSPASKTFVPRSSLSVYDKQVFRAPLVGETKADPKTYGKTLFE 480 Query: 481 NDAVRIWVSE--GQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538 DAVR WV + G++DVL+VSFKSKMNTIGP VIDGLT+AI+LAE YKGLVVWQPTSL+ Sbjct: 481 TDAVRAWVDDRAGENDVLIVSFKSKMNTIGPSVIDGLTQAIELAEKDYKGLVVWQPTSLK 540 Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598 LG PGGPFSAGANLE AMPAFMMGGAKGIEPFVK+FQ GM+RVKYASVPV+SA SGIALG Sbjct: 541 LGTPGGPFSAGANLEEAMPAFMMGGAKGIEPFVKKFQQGMLRVKYASVPVISAVSGIALG 600 Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTN-ILQFL 657 GGCEL LHSA RVA +E+Y GLVEVGVGLVPAGGGLKEAAL AA AA G+TN +L+F+ Sbjct: 601 GGCELALHSAKRVAHIESYFGLVEVGVGLVPAGGGLKEAALRAAEAATQVGATNDLLKFV 660 Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-P 716 F++AAMAKVSASAL+AR MGYL+PSD IVFNV ELL VA+ E RAL+SAGYR PL Sbjct: 661 QKSFENAAMAKVSASALDARAMGYLKPSDTIVFNVFELLDVAKKEARALSSAGYRPPLRV 720 Query: 717 TLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLA 776 T VPVAGRS IATIKASLVNMRDG FIS HDFLIASRIAEAVCGGDVEAGSLV E+WLL Sbjct: 721 TQVPVAGRSAIATIKASLVNMRDGRFISEHDFLIASRIAEAVCGGDVEAGSLVDEEWLLQ 780 Query: 777 LERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 LER+AFVDLLGT KTQERIMGMLQTGKPVRN Sbjct: 781 LERRAFVDLLGTQKTQERIMGMLQTGKPVRN 811 Lambda K H 0.319 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1773 Number of extensions: 67 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 807 Length of database: 811 Length adjustment: 41 Effective length of query: 766 Effective length of database: 770 Effective search space: 589820 Effective search space used: 589820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory